Clear cell odontogenic tumor, a rare epithelial jaw lesion of putative odontogenic origin, histologically resembles clear cell adenocarcinomas. Ultrastructural and histochemical features are described and support a non-glandular derivation. The intraosseous neoplasm is characterized by ovoid nests of clear or finely stippled cells with a mature collagenous stroma. These cells are PAS-positive, diastase labile and fail to bind alcian blue. Enzyme histochemical reactions disclose dehydrogenase, non-specific esterase, and acid phosphatase positivity. Fine structural characteristics include plasma membrane microvilli, desmosomes, endoplasmic reticulum, free ribosomes, glycogen rosettes and lysosomes. Many cells exhibit a paucity of cytoplasmic organelles with prominent vacuolization. Centrioles and annulate lamellae are also encountered. Summarily, clinical, radiographic, histochemical and ultrastructural features indicate that this neoplasm is probably of epithelial odontogenic origin with cytodifferentiation emulating glycogen-rich presecretory ameloblasts.